วีดีโอ

In addition to a nice single particle cryo-EM GUI, cisTEM also comes with programs that you may find useful in your own data analysis. cisTEM vs 1.0 beta (discussed in this video) has ~40 of these programs that can be used to do things like, calculate an FSC, resize a volume, change a volumes pixel size and so on. In this video I introduce documentation that describes reference material for the...

Some details about each of the parameters needed for the introductory portion of the tutorial.

Using the real space image, cummulative convolution map, and 3d model, rapidly edit template matching results.

create the project subTomoMeta, which is the binary file tracking the project, create and in initial average, evaluate FSC to confirm gold-standard compliance and final check on the average from each tomo to ensure quality. Set-up and run alignment.

select a template, scale as necessary and define relevant parameters to find the initial coordinates and euler angles for the subtomograms in your sample.

Limits in x,y,z for each sub area are needed by emClarity for reconstructing tomograms as needed during subTomogram processing. Using this script makes defining those boundaries straightforward, and also provides an initial survey of the quality of the data.

an initial estimate of the ctf provides a good measure of the quality of each given data set, and will be necessary to move on after template matching. This also creates a copy of the aligned stack to be used for initial tomogram reconstructions.

After obtaining the tutorial data (or your own data later on) and setting up your project directory the next step is to estimate the tilt-series geometry and also obtain a model describing the location of any gold-fiducial markers to later be erased.

describes where and how to find information to use gpu accelerated software for the enhanced macromolecular classification and alignment for high-resolution in situ tomography.

Fitting a PDB into an EM density should be rapid and easy. This is one way to make that happen. Edits: Around 3:30 the affine transform in Chimera's results dialog is obviously 4x4 not 4x1 as I mis-stated. Also the translational displacement is in Angstroms, not in pixels.